Aziz Nurnadia Marshita Abdul, Esa Yuzine, Arshad Aziz
J Environ Biol. 2016 Jul;37(4 Spec No):725-33.
The present study was carried out to examine the species identification and phylogenetic relationships of groupers in Malaysia using mitochondrial Cytochrome c Oxidase I (COI) gene, commonly known as barcoding gene. A total of 63 individuals comprising 10 species from three genera were collected from the coastal areas of Johor, Kelantan, Pahang, Perak, Selangor and Terengganu. All the individuals were morphologically identified and molecular works involved polymerase chain reaction (PCR) and sequencing of COI barcoding fragment (655 base pairs). Results from the BLAST search showed that 55 sequences could be assigned to 10 grouper species with high percentage identity index (≥95% to 100%), while eight grouper individuals showed discrepancies in their taxonomic identification based on the morphology and the COI barcoding results. The histogram of distances showed that there was a clear-cut barcode gap present in the sequences indicating a clear separation between intraspecific and interspecific distances. The pairwise genetic distances showed lowest pairwise distance between P. leopardus and P. maculatus (4.4%), while the highest pairwise distance was between E. bleekeri and P. maculatus (23.5%), supporting their morphological and habitat similarities and differences. Phylogenetic analysis (Neighbor-Joining) showed the presence of two major clades (1) genus Epinephelus vs (2) genus Plectropomus and Cephalopholis). In conclusion, the present study has managed to show the accuracy of DNA barcoding method for species identification, and utilization of COI gene for phylogenetic study among groupers. ?
本研究旨在利用线粒体细胞色素c氧化酶I（COI）基因（通常称为条形码基因）来检测马来西亚石斑鱼的物种鉴定和系统发育关系。从柔佛州、吉兰丹州、彭亨州、霹雳州、雪兰莪州和登嘉楼州的沿海地区共收集了63个个体，包括来自三个属的10个物种。所有个体均经过形态学鉴定，分子工作包括聚合酶链反应（PCR）和COI条形码片段（655个碱基对）的测序。BLAST搜索结果显示，55个序列可被归为10种石斑鱼，具有较高的百分比同一性指数（≥95%至100%），而8个石斑鱼个体在基于形态学和COI条形码结果的分类鉴定上存在差异。距离直方图显示，序列中存在明显的条形码间隙，表明种内和种间距离有明显区分。成对遗传距离显示，豹纹石斑鱼和点带石斑鱼之间的成对距离最低（4.4%），而布氏石斑鱼和点带石斑鱼之间的成对距离最高（23.5%），这支持了它们在形态和栖息地方面的异同。系统发育分析（邻接法）显示存在两个主要分支（1）石斑鱼属与（2）九棘鲈属和侧牙鲈属）。总之，本研究成功展示了DNA条形码方法在物种鉴定中的准确性，以及COI基因在石斑鱼系统发育研究中的应用。
